2ec5
Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin
SAXS 散射曲线 SAXS Profile
P(r) 距离分布 P(r) Distribution
1. 结构基本信息 1. Structure Basics
| 条目编号 entry_id | 2ec5 |
| 沉积日期 deposition_date | 2007-02-09 |
| 结构标题 title | Crystal structures reveal a thiol-protease like catalytic triad in the C-terminal region of Pasteurella multocida toxin |
| 关键词 keywords | Pasteurella multocida toxin, Cys1159Ser mutant, inactivated mutant, TOXIN; TOXIN |
| 实验方法 method | X-RAY DIFFRACTION |
2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)
| 回转半径 Rg (Guinier) rg_guinier | 43.97 Å |
| 回转半径 Rg (电子) rg_electron | 43.59 Å |
| 零角强度 I(0) i0 | 369637000.00 |
| 分子量 molecular_weight | 160160.0 kDa |
| 排除体积 excluded_volume | 201390 ų |
| 包络体积 envelope_volume | 284640 ų |
| 水化壳体积 shell_volume | 56062 ų |
| 包络直径 envelope_diameter | 144.3 Å |
| 壳层 Rg shell_rg | 46.90 Å |
| 包络 Rg envelope_rg | 42.73 Å |
| 形状 Rg shape_rg | 43.59 Å |
| 总 Rg total_rg | 43.74 Å |
| 总原子数 total_atoms | 11286 |
| 残基数 n_residues | 1422 |
| 球谐函数阶数 n_harmonics | 20 |
| q 范围 q_range | — – 0.5000 Å−1 |
| 数据点数 n_points | 101 |
| 壳层类型 shell_type | directional |
| 溶剂电子密度 solvent_density | 0.3340 e/ų |
| 壳层衬度 contrast_shell | 0.0300 e/ų |
| CRYSOL 版本 crysol_version | 4.1.3 |
3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)
| 最大尺寸 Dmax dmax | 140.6 Å |
| Rg (实空间) rg_real | 43.95 Å |
| Rg 误差 (实空间) rg_real_error | 1.00 Å |
| I(0) (实空间) i0_real | 3.6960e+08 |
| I(0) 误差 (实空间) i0_real_error | 6.3690e+06 |
| Rg (倒空间) rg_reciprocal | 43.97 Å |
| I(0) (倒空间) i0_reciprocal | 369600000.0000 |
| 解质量估计 total_estimate | 0.8946 |
| 解质量评级 solution_quality | GOOD a GOOD solution |
| P(r) 峰数 n_peaks | 1 |
| 主峰位置 r_peak_primary | 50.8 Å |
| 偏度 Skewness skewness | 0.213 |
| 峰度 Kurtosis kurtosis | -0.626 |
| 角度范围 angular_range | — – 0.1800 Å−1 |
| 当前正则化参数 α current_alpha | 0.0000 |
| 最高正则化参数 α highest_alpha | 19460000.0000 |
| 实空间数据点数 n_real_points | 37 |
| GNOM 版本 gnom_version | 4.1.3 |
| 质量判据 quality_criteria | AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.770 |
4. 晶体学与实验 4. Crystallography & Experiment
5. 实体与聚合体信息 (2)
6. 折叠分类 (SCOP + CATH) 12 domains
SCOP 2.08 (6 domains)
| 结构域编号 domain_id | d2ec5a1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.296 — PMT central region-like |
| 超家族 Superfamily superfamily | a.296.1 — PMT central region-like |
| 家族 Family family | a.296.1.1 — PMT central region-like |
| 结构域编号 domain_id | d2ec5a2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.150 — EreA/ChaN-like |
| 超家族 Superfamily superfamily | c.150.1 — EreA/ChaN-like |
| 家族 Family family | c.150.1.2 — PMT domain-like |
| 结构域编号 domain_id | d2ec5a3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.3 — Cysteine proteinases |
| 超家族 Superfamily superfamily | d.3.1 — Cysteine proteinases |
| 家族 Family family | d.3.1.17 — PMT C-terminal domain like |
| 结构域编号 domain_id | d2ec5b1 |
| 类 Class class | a — All alpha proteins |
| 折叠类型 Fold fold | a.296 — PMT central region-like |
| 超家族 Superfamily superfamily | a.296.1 — PMT central region-like |
| 家族 Family family | a.296.1.1 — PMT central region-like |
| 结构域编号 domain_id | d2ec5b2 |
| 类 Class class | c — Alpha and beta proteins (a/b) |
| 折叠类型 Fold fold | c.150 — EreA/ChaN-like |
| 超家族 Superfamily superfamily | c.150.1 — EreA/ChaN-like |
| 家族 Family family | c.150.1.2 — PMT domain-like |
| 结构域编号 domain_id | d2ec5b3 |
| 类 Class class | d — Alpha and beta proteins (a+b) |
| 折叠类型 Fold fold | d.3 — Cysteine proteinases |
| 超家族 Superfamily superfamily | d.3.1 — Cysteine proteinases |
| 家族 Family family | d.3.1.17 — PMT C-terminal domain like |
CATH v4.4 (6 domains)
| 结构域编号 domain_id | 2ec5A01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 670 — Secreted effector protein ssei fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Secreted effector protein ssei. |
| 结构域编号 domain_id | 2ec5A02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 180 — |
| 结构域编号 domain_id | 2ec5A04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 11550 — |
| 结构域编号 domain_id | 2ec5B01 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 10 — Roll |
| 拓扑 Topology topology | 670 — Secreted effector protein ssei fold |
| 同源超家族 H-superfamily homologous superfamily | 10 — Secreted effector protein ssei. |
| 结构域编号 domain_id | 2ec5B02 |
| 类 Class class | 1 — Mainly Alpha |
| 架构 Architecture architecture | 20 — Up-down Bundle |
| 拓扑 Topology topology | 140 — Butyryl-CoA Dehydrogenase, subunit A; domain 3 |
| 同源超家族 H-superfamily homologous superfamily | 180 — |
| 结构域编号 domain_id | 2ec5B04 |
| 类 Class class | 3 — Alpha Beta |
| 架构 Architecture architecture | 40 — 3-Layer(aba) Sandwich |
| 拓扑 Topology topology | 50 — Rossmann fold |
| 同源超家族 H-superfamily homologous superfamily | 11550 — |